What is Phoenix?
Phoenix is a variant annotation and filtering tool capable of processing billions of variants from multiple species.
How to Use Phoenix (Getting Started)
General Flow:
- Build Your Cohort: Select the specific samples you want to analyze.
- Filter Variants: Narrow down the list of variants based on desired criteria.
- Explore Individual Variants: Attach custom notes or metadata to variants. Browse variant location with UCSC Genome Browser.
- Add Variants to Cart: Move the variants you want to keep to your final selection cart.
- Iterate: Repeat steps 2-4 to refine your selection.
- Save and Manage Your Work: View your final cart selection and save it for future use or export.
Specific Steps:
Step 1: Build Your Cohort
The cohort is the starting point for all analysis. It defines the set of variants you will work with.
Step 2: Filter Variants
After building your cohort, you will refine the millions of genetic variants down to a manageable list using various filtering tools:
- Basic Column Filters: Most columns can be filtered based on their types with common comparators.
- Advanced Filters (Filter Panel): A set of frequently used filters with customized selectors. Also a place to filter by fields not present in the table (e.g., Regions and Phenotypes).
- AI Filtering: An experimental feature to help set column filters with natural language. [Video tutorial coming soon]
Step 3: Explore Individual Variants
- Adding annotations: You can write annotation cards for any variants. Those annotations will be displayed in other variants if they match the same scope (e.g., same species or region).. Select a variant and click the "Add Annotation" button to create a custom note. [Video tutorial coming soon]
- Viewing annotations: Annotations appear on matching variants throughout your analysis based on an annotation scope. (see FAQ about scopes and in the video above)
- Open a variant location with UCSC Genome Browser:
- From the Target Selection Page:
- From the Variant Details Page
Step 4: Add Variants to Your Cart
- Add a single variant to the cart: Select the variant's row and click the "Add to Cart" icon.
- Add all filtered variants to cart: Use the bulk action button to add the entire filtered list. (Note: This action has a limit of 1,000 variants per batch.)
Step 6: Saving and Managing Your Work
Saving Your Variant Selection:
- Navigate to the Cart view.
- Review your final list of variants.
- Click "Save Selection" and provide a descriptive name for your file.
Manage Annotations
- You can view, edit, and delete all your annotations in one place. [Video tutorial coming soon]
Continue Work from a Previously Saved State:
- You can load a saved cohort from your workspace to continue filtering.
Finding Your Saved Variants:
FAQ (Frequently Asked Questions)
This section will be populated with common questions sourced from messages and Slack.
Can I arrange and resize columns in Target Selection?
You sure can! Click below for tips and tricks for customizing tables.
What is an annotation scope?
An annotation scope is a way for users to decide where the annotation information applies. A variant displays annotations (written by you or other users) that match each annotation scope with the variant information (for example, its location on the genome, or its species).
The current scopes are:
- Variant Scope: a variant must shares the same Species, Genome, Chr, Position, REF, and ALT as a variant scoped annotation to see it.
- Species Scope: a variant must share the same species as a species scoped annotation to see it .
- Region Scope: a variant must fall inside the selected region start-end (inclusive) and have the same Genome, and Chromosome as a region scoped annotation.
- Phenotype Scope: a variant must fall inside any of the regions associated with a phenotype or its descendants. It’s basically a multi-region scope. Which regions are associated with a phenotype is a combination of pre-loaded regions and variant locations tagged by users with that phenotype (see Phenotype Tagging).